HapEdit: An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Jong Hyun Kim, Woo Cheol Kim, Lei M. Li, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

Abstract

The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.

Original languageEnglish
Pages (from-to)W557-W561
JournalNucleic acids research
Volume39
Issue numberSUPPL. 2
DOIs
Publication statusPublished - 2011 Jul 1

Bibliographical note

Funding Information:
The National Research Foundation of Korea (2009-0083311 to J.H.K., W.K. and S.P.; 2011-0004382 to S.P.); The National Institutes of Health, USA (HG002790 to L.M.L.). Funding for open access charge: The National Research Foundation of Korea [2009-0083311].

All Science Journal Classification (ASJC) codes

  • Genetics

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